Frequently Asked Questions

Does SHORE include the SHOREmap package for mutation mapping?

No. SHOREmap is an add-on that is distributed as a separate package. However, SHOREmap requires the output of shore consensus as an input.

What happened if I received a bad write error?

• read/write failure --- bad write

• thread N: error - bad write
terminate called after throwing an instance of 'std::ios_base::failure'

These errors indicate a failure writing to disk, usually after running out of disk space either in the temporary file directory or in your output directory.

To reduce disk space requirements for read import and alignment, try adding the -B switch to shore import, e. g. shore import -B 1000000 ...; or provide an alternate temporary file directory with sufficient disk space, e. g. shore -T /very_large_tmp mapflowcell ....